goldenflaw

You should use the -s flag with the appropriate setting depending on your RNA-seq library. Best, Yang On Wed, May 19, 2021 at 8:41 AM hkmztrk ***@***.***> wrote: > @geng-lee...

If I recall correctly, the confounder effect is estimated from fitting the parameters of the dirichlet multinomial: e.g. x_i * beta_j + confounder * beta_confounder + u_j below. It is...

Hi, LeafCutter relies on accurate alignments, as such if the aligned reads are wrong then LeafCutter output will be wrong too. I would suggest you to check your read alignments....

Have you tried https://github.com/davidaknowles/leafcutter/issues/160 or https://github.com/davidaknowles/leafcutter/issues/188?

Could you check whether all your libraries have mapped successfully, with reads on each chromosome? Best, Yang On Thu, May 13, 2021 at 9:58 AM jaro-slamecka ***@***.***> wrote: > Hi,...

Would you be able to post the entire error that you are encountering? Best, Yang On Thu, May 13, 2021 at 11:02 AM jaro-slamecka ***@***.***> wrote: > I checked with...

Are you running regtools correctly? There shouldn't be 20:? (which means that some reads have unassigned strands). Best, Yang On Thu, May 13, 2021 at 11:29 AM jaro-slamecka ***@***.***> wrote:...

If I recall correctly, regtools may have updated their options, see https://regtools.readthedocs.io/en/latest/commands/junctions-extract/. You could try to re-run using the newer options paying attention to the -s flag. Best, Yang On...

Throw them out. Best, Yang On Thu, May 13, 2021, 18:40 jaro-slamecka ***@***.***> wrote: > Just looked into the script again and actually, that's what I used, I > think...

Try using the -chrom flag or removing GL/KI chromosomes. Best, Yang On Thu, Jun 10, 2021 at 2:12 PM Ying ***@***.***> wrote: > I run into the same problems, and...